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- PDB-4rf9: Crystal structure of double-domain arginine kinase from Anthopleu... -

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Basic information

Entry
Database: PDB / ID: 4rf9
TitleCrystal structure of double-domain arginine kinase from Anthopleura japonicas in complex with L-arginine and ATPgS
ComponentsArginine kinase
KeywordsTRANSFERASE / double domain / tandem domain / phosphagen kinase
Function / homology
Function and homology information


arginine kinase / arginine kinase activity / phosphocreatine biosynthetic process / creatine kinase activity / phosphorylation / ATP binding
Similarity search - Function
Transferase Creatine Kinase; Chain A, domain 1 / ATP:guanido phosphotransferase, N-terminal domain / ATP:guanido phosphotransferase, N-terminal / ATP:guanido phosphotransferase, N-terminal domain superfamily / ATP:guanido phosphotransferase, N-terminal domain / Phosphagen kinase N-terminal domain profile. / ATP:guanido phosphotransferase active site / Phosphagen kinase active site signature. / ATP:guanido phosphotransferase / ATP:guanido phosphotransferase, catalytic domain ...Transferase Creatine Kinase; Chain A, domain 1 / ATP:guanido phosphotransferase, N-terminal domain / ATP:guanido phosphotransferase, N-terminal / ATP:guanido phosphotransferase, N-terminal domain superfamily / ATP:guanido phosphotransferase, N-terminal domain / Phosphagen kinase N-terminal domain profile. / ATP:guanido phosphotransferase active site / Phosphagen kinase active site signature. / ATP:guanido phosphotransferase / ATP:guanido phosphotransferase, catalytic domain / ATP:guanido phosphotransferase, C-terminal catalytic domain / Phosphagen kinase C-terminal domain profile. / Glutamine synthetase/guanido kinase, catalytic domain / Creatine Kinase; Chain A, domain 2 / Glutamine synthetase/guanido kinase, catalytic domain / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ARGININE / Arginine kinase
Similarity search - Component
Biological speciesAnthopleura japonica (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsWang, Z. / Qiao, Z. / Ye, S. / Zhang, R.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structure of a double-domain phosphagen kinase reveals an asymmetric arrangement of the tandem domains.
Authors: Wang, Z. / Qiao, Z. / Ye, S. / Zhang, R.
History
DepositionSep 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Arginine kinase
B: Arginine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,8767
Polymers160,8852
Non-polymers9925
Water10,287571
1
A: Arginine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,6182
Polymers80,4421
Non-polymers1751
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Arginine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,2595
Polymers80,4421
Non-polymers8174
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.263, 59.483, 162.148
Angle α, β, γ (deg.)90.00, 91.36, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Arginine kinase / / AK


Mass: 80442.328 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anthopleura japonica (sea anemone) / Production host: Escherichia coli (E. coli) / References: UniProt: O15992, arginine kinase
#2: Chemical ChemComp-ARG / ARGININE / Arginine


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N4O2
#3: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 571 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.55 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.8
Details: 20mM HEPES, 50mM NaCl, 10mM L-arginine, 10mM ATPgS, 0.2M Potassium Acetate, 20% PEG3350, pH 7.8, VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.35→48 Å / Num. all: 62383 / Num. obs: 60449 / % possible obs: 96.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.35→2.39 Å / % possible all: 98.6

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIX(phenix.phaser)model building
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4RF6

4rf6


Resolution: 2.35→47.955 Å / SU ML: 0.29 / σ(F): 1.33 / Phase error: 29.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2477 3036 5.05 %
Rwork0.1993 --
obs0.2017 60158 95.38 %
all-63069 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→47.955 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10878 0 63 571 11512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311169
X-RAY DIFFRACTIONf_angle_d0.70215062
X-RAY DIFFRACTIONf_dihedral_angle_d12.8784235
X-RAY DIFFRACTIONf_chiral_restr0.0471632
X-RAY DIFFRACTIONf_plane_restr0.0041957
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.38210.3575990.26342071X-RAY DIFFRACTION75
2.3821-2.42120.31031260.25432635X-RAY DIFFRACTION99
2.4212-2.46290.27131530.25072661X-RAY DIFFRACTION98
2.4629-2.50770.3071560.24922628X-RAY DIFFRACTION98
2.5077-2.55590.31561470.25572632X-RAY DIFFRACTION98
2.5559-2.60810.3161240.26052687X-RAY DIFFRACTION98
2.6081-2.66480.4231430.32522591X-RAY DIFFRACTION97
2.6648-2.72680.35151290.27952639X-RAY DIFFRACTION97
2.7268-2.7950.41841310.28112658X-RAY DIFFRACTION97
2.795-2.87050.34861240.24512589X-RAY DIFFRACTION96
2.8705-2.9550.34931460.23982622X-RAY DIFFRACTION97
2.955-3.05030.30981420.22332593X-RAY DIFFRACTION97
3.0503-3.15930.30131460.21762631X-RAY DIFFRACTION96
3.1593-3.28580.25791300.2242646X-RAY DIFFRACTION97
3.2858-3.43530.26261470.19952587X-RAY DIFFRACTION97
3.4353-3.61640.27361340.19082632X-RAY DIFFRACTION96
3.6164-3.84290.22431550.17822564X-RAY DIFFRACTION95
3.8429-4.13940.19861350.172588X-RAY DIFFRACTION94
4.1394-4.55570.19631350.15452486X-RAY DIFFRACTION91
4.5557-5.21420.20991370.16562574X-RAY DIFFRACTION94
5.2142-6.56670.21591540.18892706X-RAY DIFFRACTION98
6.5667-47.96460.18621430.17432702X-RAY DIFFRACTION95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1526-0.36310.03682.2279-0.6141.95430.18030.3730.1342-0.4633-0.1374-0.34690.33480.4471-0.04260.39910.10670.0980.49270.02610.359629.00379.1606-29.212
21.052-0.330.18040.9486-0.21262.16040.0344-0.16670.0587-0.06990.06550.04680.1392-0.1427-0.08980.2499-0.00780.04350.29760.02680.252816.46929.904-5.5118
30.29930.07530.89160.24030.89433.18880.230.1975-0.10110.11280.0722-0.24820.88140.8171-0.20610.3920.133-0.01580.46110.02720.409937.20484.193518.6142
41.3204-0.3355-0.02261.01290.85123.31650.02040.21130.1964-0.2339-0.1108-0.0957-0.6498-0.06990.06970.30730.01950.02740.2930.07370.331424.026626.900431.7393
50.6714-0.4237-0.00461.56990.57971.31630.07070.0760.1552-0.3512-0.1485-0.2206-0.5278-0.33880.04350.3420.0680.0320.27380.03850.306820.005130.766537.7535
60.77040.6461-0.37710.5792-0.29240.3215-0.1493-0.23350.5224-0.17960.2313-0.8865-0.32590.0304-0.10760.4308-0.05360.00670.3046-0.05710.90930.509943.446548.0218
70.8451-0.290.29271.5758-0.66962.2217-0.0430.0411-0.0171-0.1403-0.0442-0.07720.228-0.07160.06710.23590.00370.00950.2199-0.0120.25171.878728.9908122.1567
80.39730.3191-0.57480.3736-0.46192.54920.1690.02710.16830.0572-0.0120.0806-0.7933-0.481-0.06680.6020.12690.00360.34830.00670.36752.153349.344195.3902
90.6242-0.6595-0.71941.26010.19682.3415-0.1336-0.20290.05640.41360.0722-0.220.01980.18170.06140.40670.0249-0.1450.2742-0.0150.307223.016230.331875.203
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:63 )A1 - 63
2X-RAY DIFFRACTION2( CHAIN A AND RESID 64:290 )A64 - 290
3X-RAY DIFFRACTION3( CHAIN A AND RESID 291:405 )A291 - 405
4X-RAY DIFFRACTION4( CHAIN A AND RESID 406:578 )A406 - 578
5X-RAY DIFFRACTION5( CHAIN A AND RESID 579:642 )A579 - 642
6X-RAY DIFFRACTION6( CHAIN A AND RESID 643:712 )A643 - 712
7X-RAY DIFFRACTION7( CHAIN B AND RESID 1:290 )B1 - 290
8X-RAY DIFFRACTION8( CHAIN B AND RESID 291:393 )B291 - 393
9X-RAY DIFFRACTION9( CHAIN B AND RESID 394:712 )B394 - 712

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